Medical and social importance of congenital and hereditary diseases requires improving preventive measures such as prenatal diagnosis (PD). Results of the audit of the new PD system of congenital malformations and frequent chromosomal abnormalities (CA), which was gradually introduced in the regions of the Russian Federation since 2010 as a part of the national priority project «Health», are presented. International experience and the recommendation of an independent medical organization Fetal Medicine Foundation, UK (FMF) formed the basis of a new algorithm of early prenatal screening in Russia. During the work on the project major problems were solved: the creation of regional systems of expert-level diagnostics, special training and validation of competences of expert doctors to perform ultrasound examinations in 11—14 weeks gestation, the use of a single software that allows to calculate the individual risk of CA by a combination of ultrasound and biochemical data and to carry out internal and external audits of all prenatal measurements.